Seeing what's going on with Facebook and Google I guess Apple didn't pay much attention to this.
In both Google and Facebook's cases, they were using it to distribute apps to the public at large (i.e., users with whom they have no business relationship) simply because they couldn't get the apps into the app store to begin with because they would otherwise violate Apple's rules. So not only were they flagrantly disregarding the ToS of their enterprise certs, they were doing so in order to violate Apple's rules for app distribution. Less than great.
I mean, the program exists for a reason.
The whole point of enterprise certificates was to allow creation of internal apps that even Apple shouldn't know about.
I think most/all of the companies in the program would say it's about controlling the distribution of their apps, since putting them on the App Store would expose them to the public, and less about hiding from Apple...